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RNA Families
A survey of nematode SmY RNAs
Thomas A. Jones , Wolfgang Otto, Manja Marz , Sean R. Eddy and Peter F. Stadler
Volume 6, Issue 1January/February/March 2009
Pages: 5 - 8
This is an open-access article
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SmY RNAs are a family of ~70–90 nt small nuclear RNAs found in nematodes. In C. elegans, SmY RNAs copurify in a small ribonucleoprotein (snRNP) complex related to the SL1 and SL2 snRNPs that are involved in nematode mRNA trans-splicing. Here we describe a comprehensive computational analysis of SmY RNA homologs found in the currently available genome sequences. We identify homologs in all sequenced nematode genomes in class Chromadorea. We are unable to identify homologs in a more distantly related nematode species, Trichinella spiralis (class: Dorylaimia), and in representatives of non-nematode phyla that use trans-splicing. Using comparative RNA sequence analysis, we infer a conserved consensus SmY RNA secondary structure consisting of two stems flanking a consensus Sm protein binding site. A representative seed alignment of the SmY RNA family, annotated with the inferred consensus secondary structure, has been deposited with the Rfam RNA families database.
Authors
Thomas A. Jones
HHMI Janelia Farm Research Campus; Ashburn Virginia 20147;USA
Wolfgang Otto
University of Leipzig; Leipzig 04107 Germany
Manja Marz
University of Leipzig; Leipzig 04107 Germany
Sean R. Eddy
HHMI Janelia Farm Research Campus; Ashburn Virginia 20147;USA
Peter F. Stadler
University of Leipzig; Leipzig, Germany
This is an open-access article
Download PDFIf the document does not open, please right-click on the link (control-click on a Macintosh) and select the option to save the file to disk.
